Scientists Reconstruct the Genome of the 180-Million-Year-Old Common Ancestor of All Mammals

By UNIVERSITY OF CALIFORNIA - DAVIS OCTOBER 15, 2022

The mammal ancestor had 19 autosomal chromosomes and 2 sex chromosomes.

University of California, Davis scientists help reveal the genome of the common ancestor of all mammals

From a platypus to a blue whale, all living mammals today are descended from a common ancestor that existed some 180 million years ago. Although we don’t know a lot about this animal, a global team of experts has recently computationally reconstructed the organization of its genome. The findings were recently published in the journal Proceedings of the National Academy of Sciences.

“Our results have important implications for understanding the evolution of mammals and for conservation efforts,” said Harris Lewin, distinguished professor of evolution and ecology at the University of California, Davis, and senior author on the paper.

The researchers used high-quality genome sequences from 32 living species, spanning 23 of the 26 known mammalian orders. Humans and chimpanzees were among these species, as were wombats and rabbits, manatees, domestic cattle, rhinos, bats, and pangolins. The chicken and Chinese alligator genomes were also used as comparison groups in the analysis. Some of these genomes are being produced as part of the Earth BioGenome Project and other large-scale biodiversity genome sequencing initiatives. Lewin is the chair of the Earth BioGenome Project’s Working Group.

According to Joana Damas, the first author of the study and a postdoctoral researcher at the UC Davis Genome Center, the mammal ancestor had 19 autosomal chromosomes, which control the inheritance of an organism’s characteristics other than those controlled by sex-linked chromosomes (these are paired in most cells, making 38 in total), plus two sex chromosomes. The researchers identified 1,215 blocks of genes that appear on the same chromosome in the same order across all 32 genomes. Damas said that these building blocks of all mammal genomes include genes that are essential for the development of a normal embryo.

Chromosomes stable for over 300 million years

The researchers found nine whole chromosomes or chromosome fragments in the mammal ancestor whose order of genes is the same in modern birds’ chromosomes.

“This remarkable finding shows the evolutionary stability of the order and orientation of genes on chromosomes over an extended evolutionary timeframe of more than 320 million years,” Lewin said.

In contrast, regions between these conserved blocks contained more repetitive sequences and were more prone to breakages, rearrangements, and sequence duplications, which are major drivers of genome evolution.

“Ancestral genome reconstructions are critical to interpreting where and why selective pressures vary across genomes. This study establishes a clear relationship between chromatin architecture, gene regulation, and linkage conservation,” said Professor William Murphy, Texas A&M University, who was not an author of the paper. “This provides the foundation for assessing the role of natural selection in chromosome evolution across the mammalian tree of life.”

The researchers were able to follow the ancestral chromosomes forward in time from the common ancestor. They found that the rate of chromosome rearrangement differed between mammal lineages. For example, in the ruminant lineage (leading to modern cattle, sheep, and deer) there was an acceleration in rearrangement 66 million years ago when an asteroid impact killed off the dinosaurs and led to the rise of mammals

The results will help to understand the genetics behind adaptations that have allowed mammals to flourish on a changing planet over the last 180 million years, the authors said.

Reference: “Evolution of the ancestral mammalian karyotype and syntenic regions” by Joana Damas, Marco Corbo, Jaebum Kim, Jason Turner-Maier, Marta Farré, Denis M. Larkin, Oliver A. Ryder, Cynthia Steiner, Marlys L. Houck, Shaune Hall, Lily Shiue, Stephen Thomas, Thomas Swale, Mark Daly, Jonas Korlach, Marcela Uliano-Silva, Camila J. Mazzoni, Bruce W. Birren, Diane P. Genereux, Jeremy Johnson, Kerstin Lindblad-Toh, Elinor K. Karlsson, Martin T. Nweeia, Rebecca N. Johnson, Zoonomia Consortium and Harris A. Lewin, 26 September 2022, Proceedings of the National Academy of Sciences.
DOI: 10.1073/pnas.2209139119

The study was funded by the National Institutes of Health and the U.S. Department of Agriculture.